(Excerpt from MS thesis of Susan K. Robbins, Marine Sciences Research Center, 1977)

General Description

Stony Brook Harbor is located on the north shore of Long Island on the boundary of Smithtown and Brookhaven Townships with over 90 percent in Smithtown, in western Suffolk County. It is a broad, shallow, roughly L-shaped body of water Separated from Long Island Sound by two baymouth bars, Long Beach and West Meadow Beach, a narrow inlet (app. 130 m or 400 ft wide) at its northeastern corner connects the harbor with Smithtown Bay. West Meadow Creek, which is located behind West Meadow Beach, is the principal tributary, entering the harbor near the inlet.

The harbor's drainage basin consists of rolling, wooded hills with low density residential development and much open space. The only site of intensive development is the commercial portion of Stony Brook village, near the entrance to the harbor.

Stony Brook Harbor is a recreational waterbody, used for activities such as boating, clamming, swimming and fishing. There is no industry anywhere on the shoreline and only one parcel zoned for industrial use in the drainage basin. It is probably the least spoiled (closest to natural condition) of any of the harbors on the north shore of Long Island. It is also an historic resource, listed in the New York State Division of Historic Preservation's Historic Resources Survey as an Historic and Natural District.

Geological Structure and History

The north shore of Long Island is classified as a primary coast: one whose character is due to the sea level coming to rest against a land form that was the result of terrestrial agencies. In this case, the terrestrial agency is glacial deposition and the partially submerged land form is a moraine. The action of waves and currents has modified the configuration of the north shore in the area of Stony Brook Harbor through the formation of baymouth bars which separate the harbor from Long Island Sound.

Stony Brook Harbor is relatively young geologically. Its origin can be traced back only as far as the late Cretaceous or the early Tertiary periods (app. 60 to 70 million years before present). At that time, a northerly flowing stream, draining into what is now Long Island Sound, cut a valley through sedimentary deposits laid down earlier in the Cretaceous. During the Pleistocene epoch (app. 3 million to 10,000 years before present), glacial action scoured out the valley, enlarging it and giving it its present broad, smooth shape.

The upland surrounding the harbor is composed of glacial drift deposited during the most recent stage of glaciation, the Wisconsin. These deposits are part of the Harbor Hill moraine, the ridge which runs roughly east-west along almost the entire length of Long Island, forming the hilly topography of the north shore.

The youngest geological features of Stony Brook Harbor are the baymouth bars and the marshes behind them. As sea level rose following the retreat of the last glaciation, wave and current action eroded the bluffs and beaches at Nissequogue and Crane Neck. The longshore current carried some of the eroded material (mostly the sand fraction) east from Nissequogue and south from Crane Neck point, forming, respectively, Long Beach and West Meadow Beach.

In the calm waters behind the bars, salt marsh plants could take root and grow. As these plants trapped fine sediments carried in on the tide, the salt marsh expanded, growing both in level, in response to rising sea level, and in areal extent.

Physical Description

Stony Brook Harbor and its major tributary, West Meadow Creek, cover an area of 4.8 km2, approximately 3.0 km2 of open water and 1.8 km2 of island and marsh.

They have roughly 23 km of shoreline. Their average depth at mean low water is only about 0.9 m. West Meadow Creek, which is tidal for its entire length of 2.4 km, meanders from the north, entering the northeastern corner of the harbor near the inlet. The other tidal creek, Stony Brook Creek (the "mill creek"), enters the harbor in the southeastern corner. About 0.4 km upstream is a mill dam, forming two ponds which flow one into the other; a small upper pond and the mill pond. The creek is little more than a trickle at low tide as it passes through the marsh at its mouth. A small watercourse, dry most of the year, feeds into the extreme southern end (the head) of the harbor. It carries runoff from the land during spring thaw and rainstorms.

There are two major channels in Stony Brook Harbor, both in the outer section. Porpoise Channel runs westerly from the inlet along the southern shore of Long Beach. It has been dredged for its entire length and is about 1.8 m deep at mean low water. The other channel, the "main" channel, runs southerly from the inlet to the southeastern corner of the harbor. It has also been dredged, and ranges from 2.4 to 3.7 m deep.

The channel in West Meadow Creek is shallow for most of its length, ranging from nearly 0 to 1.2 m deep, except for the two dredged areas: the northern, which is as deep as 6.1m in spots, and Aunt Amy's Creek, dredged irregularly to 0.9 to 2.4 m.

Wetlands

Much of the shoreline and most of the islands in Stony Brook Harbor support a healthy growth of salt marsh grass. Most of the western shore of West Meadow Creek is part of an extensive, well developed salt meadow, or high marsh.

There are 1.7 km2 of marine wetlands in Stony Brook Harbor and West Meadow Creek. On the 1.3 km in the harbor and Stony Brook Creek, 98 percent of the vegetation is Spartina alterniflora (salt marsh cord grass, or thatch), which is generally restricted to areas below MHW (intertidal marsh). The 0.4 km2 at West Meadow support a growth of 30 percent Spartina alterniflora, app. 50 percent Spartina patens (salt meadow grass, or salt hay) and app. 20 percent Distichlis spicata (spike grass).

The marine wetlands in their natural state perform a variety of valuable functions which affect the whole web of life:

1) Basic food production - Marsh grasses and algae carryon the energy transformation process called photosynthesis. A high yield salt marsh with S. alterniflopa as the main producing unit ranks - as one of the world's most productive natural or cultivated ecosystems.

2) Essential habitat - The marine wetlands support a variety of invertebrates, fish and wildlife. Shellfish live on or in the bottom, and finfish breed and/or live in the sheltered waters. Wildlife, especially waterfowl, nest, rest and find protection and food in the wetlands.

3)Marine nursery - Commercially and recreationally valuable finfishes such as striped bass (Morone saxatilis), bluefish (pomatomus saltatrix), fluke or summer flounder (Paraliohthys dentatus), menhaden (Brevoortia tyrannus) and winter flounder (pseudopleuronectes americanus) grow and develop in wetland areas where they find abundant food and protection.

4) Buffers to storms and sediment traps - Marine wetlands protect the upland from the destructive force of the sea by mitigating the effect of storm tides and waves. Their "growing edge" has been able to keep pace with the progressively rising sea level on the Atlantic coast because they act as sediment traps, i.e. as the tide floods the wetlands, the velocity of the water is reduced, allowing suspended sediment (mostly clay and silt size) to settle out on the marsh surface.

5) Water treatment system - Salt marshes function like a secondary sewage treatment plant. They settle out suspended matter and transform waste products into useful nutrient materials by both chemical and biological processes.

The upland watershed, or drainage basin, of Stony Brook Harbor is relatively small, covering 18 km2, or about 3.5 times the area of the harbor and West Meadow Creek. The boundaries of the drainage basin were determined on the basis of topography, i.e. the overall slope of the land within the drainage basin is downward in the direction of the harbor. The southern boundary coincides with the highest elevations of the Harbor Hill terminal moraine. The eastern and western boundaries are defined by a series of smaller ridges running along the Harbor Hill ground moraine in a roughly north-south direction.

A portion of the rain which falls in the drainage basin, and is not lost to the air by evaporation and plant transpiration (evapotranspiration), reaches the harbor as surface runoff and as groundwater underflow.

Surface runoff enters the harbor and the two creeks along their perimeters. The amount of fresh water entering the harbor as surface runoff is considered to be negligible when compared with that entering as groundwater underflow, which is the largest. Groundwater is discharged directly into the harbor and the creeks by underflow through their bottoms and around the shoreline. Groundwater also emerges at a few springs, especially where the land rises steeply from the shore and in some places feeds into small streams which flow into the harbor.

All of the West Meadow Creek area and most of the Long Beach peninsula are part of the coastal flood plain, i.e. those areas subject to tidal flooding during storms. The entire flood plain is subject to inundation during hurricanes.

Land Use

The combination of soil types and topography described above helps to make the area around Stony Brook Harbor a very scenic locale. Rolling hills and valleys covered with a dense growth of hardwood trees interspersed with gently sloping fields give variety and color to the landscape and provide fine locations for houses and small farms.

The area is overwhelmingly residential, but still retains much of its rural colonial character. A large number of fine old houses, dating from the colonial period and the early 19th Century, are still standing and in good repair. There are several acres of farmland under cultivation, and many acres of open fields and thick woodlands.

The upland within the Stony Brook Harbor drainage basin comes under the jurisdiction of four local governments: the incorporated villages of Head-of-the-Harbor and Nissequogue, in the Town of Smithtown, and the Town of Brookhaven. The two Villages and the Town of Brookhaven have the zoning power for almost all of the land within the drainage basin.

Stony Brook To the east of the harbor, the unincorporated community of Stony Brook occupies the section of the drainage basin that is within the Town of Brookhaven. It is a residential community with a long established central core surrounded by developments built largely on former farmland. The developments are composed of one-family houses on 22,500 sq. Ft lots.

The oldest part of Stony Brook, the "village", which was built up before the age of zoning, has a slightly greater building density than the developments. The old houses and churches are kept in excellent condition and the village has the air of a prosperous, 19th Century country town.

Most of the commercial property in Stony Brook is situated in small parcels along Route 25A, and in the village shopping center. The commercial establishments are mostly small shops, food stores, restaurants and professional offices. The State University of New York at Stony Brook occupies a large tract (about 4.4 km2 or 1100 acres), just south of Route 25A. The single industrial parcel in the entire drainage basin, owned by the Gyrodyne Corp. of America, straddles the boundary between Brookhaven and Smithtown on the southern boundary of the drainage basin. It is zoned "L" Industrial 1 - Light Industry. The parcel is heavily wooded and the facilities there are used mostly for office space and smaller companies that rent space from Gyrodyne. All the vacant land in Stony Brook is zoned residential.

Head-of-the-Harbor. The incorporated Village of Head-of-the-Harbor, located to the south of Stony Brook Harbor, is almost completely within the drainage basin, except for the extreme southwest corner. Like Stony Brook, Head-of-the- Harbor is a residential community. It is much less densely developed, however.

Almost all of the Village is zoned for 2 acre residential use, including the entire harbor shoreline. The Village zoning ordinance includes a special proviso for all lots fronting on Stony Brook Harbor: any structure (except a tennis court) must be built more than 100 ft from the mean high water line or 50 ft from the top edge of the bluff.

A 0.8 km2 corridor along Route 25A, known as the Mills Pond Historic District, has been placed on the National Register of Historic Places (Newsdav,5/17/74).

The tiny commercial section of the Village lies along its southern boundary, at the intersection of Route 25A and Moriches Road. No part of the Village is zoned industrial. A 0.18 km2 farm in the eastern part of the Village has sold the development rights to the land to Suffolk County, as part of the County’s Farmlands Preservation Program.

There are two nature preserves in the Village. East Farm Preserve, in the northeastern part of the Village is a 0.22 km2 tract of farm fields, meadows and woodlands, donated to the Nature Conservancy in 1970. In the southwestern section of the Village is the Butler-Huntingt9n Woods Preserve, 0.26 km2 of wooded glacial hills and ravines. This preserve extends partly into the Village of Nissequogue and partly outside of either Village.

Nissequogue.The incorporated Village of Nissequogue lies between Stony Brook Harbor to the east, the Nissequogue River to the west and Long Island Sound to the north. Only the eastern half of the Village is within the Stony Brook Harbor drainage basin. Like Head-of- the-Harbor, it is a low density residential community, except that it is zoned entirely for residential use. All of the Village within the drainage basin is zoned 2 acre minimum lot size with the exception of the Long Beach peninsula, which is zoned 1 acre minimum lot size.

The heavily treed, often steep hills o£ the eastern Village are, like the western Village, dotted with private estates and houses on large lots. There is a 0.32 km2 wildlife sanctuary, the David Weld Sanctuary, in the northern part of the Village. It is a woodland tract donated to The Nature Conservancy in 1969. A second Nature Conservancy sanctuary, the 0.06 km2 Delafield Woods, is located in the western part of the village, near the Nissequogue River. A 0.10 km2 preserve, owned by the Village of Nissequogue, lies at the eastern tip of Long Beach.

Town of Brookhaven

The entire length of West Meadow Beach, from the Village of Old Field boundary, south 2089 m (6850 ft) to Shipmen’s Point (at the Stony Brook Harbor inlet), is owned by the Town of Brookhaven, as far east as the right-of-way of Trustees Road. At the northerly end is a Town beach with parking and bath house facilities. South of the beach, app. 80 private houses and a private beach club (Brookhaven Bathing Association) occupy the shorefront property facing Smithtown Bay and the inlet.

At the southern end of West Meadow Beach, fronting on the inlet are six stone groins. The stone groins, built in 1948 and owned by New York State Dept. of Public Works, are in poor condition and partially buried in sand.

Behind West Meadow Beach is the West Meadow Creek wildlife refuge. The western shore of the creek is mostly salt marsh, in its natural state except for some "mosquito ditches", dug to drain standing water from the marsh surface. All of the salt marsh on the western shore of the creek, and some on the eastern shore (in the "Aunt Amy's Creek" area), a total of 0.38 km2(95 acres), are owned by the Ward Melville Heritage Foundation. Melville purchased the marsh land from private owners over a period of 12 years. In 1974, he donated it to the WMHO (formerly The Community Fund) to be kept in its natural state as a wildlife preserve. It has been named the "West Meadow Wetlands Wildlife Preserve." Located within the preserve, on the western shore of the creek just above Aunt Amy's Creek, is a small building housing a nature study center operated by the Three Village School District. The school district rents a 10 acre section of the preserve from the WMHO, at a nominal fee, for use as an outdoor classroom.

The northern and eastern shores of West Meadow Creek are in private ownership. The northern shore is the site of the former North Shore Horse Show Grounds, a private day school owned by the WMHO and the Old Field Club. Along the eastern shore are private houses and small, private beaches, and the site Wells' shipyard which until recently provided storage and repair services for small boats.

At the mouth of West Meadow Creek, where it empties into Stony Brook Harbor, begins the Stony Brook village waterfront. The small sand Street Beach, owned by the Town of Brookhaven, occupies the shoreline below the sand bluff. Farther to the south, where the shoreline swings to the west, are the Town owned floating dock, a parking lot and boat launching ramp. Adjacent to these facilities is the Stony Brook Yacht Club, a private establishment with berths for many boats. On the filled area to the southwest of the Yacht Club, where Stony Brook Creek enters the harbor, is a privately owned boat repair and marine supply business.

Town of Smithtown

The remainder of the harbor shoreline is in the Villages of Head-of-the-Harbor and Nissequogue, which are within the Town of Smithtown. From the Stony Brook Creek westward, the shoreline in Head-of-the- Harbor is all privately owned, with one exception: the small Town of Smithtown beach at the base of Cordwood Path (Cordwood Path Beach), near the Nissequogue Village boundary. Most of the shoreline within Head-of-the-Harbor is divided into private estates (ranging in size from 23 to 50 acres each) and houses on large lots (3 to 5 acres).

The western shoreline, in the Village of Nissequogue, is completely in private ownership. Here, as in Head-of-the-Harbor, large estates (between 20 and 30 acres each) line much of the shoreline. Some of the shoreline has been divided into smaller lots, of from 2 to 7 acres in size.

Halfway up the shoreline is the 0.4 km2 (102 acre) private Nissequogue Golf Club (formerly an estate). In the northwest corner of the harbor, still in the Village of Nissequogue, is the 0.2 km2 (60 acre) campus of the Knox School, a preparatory school, which was formerly a private estate. There are only about 35 houses on the 9 km (5.6 mi) of shoreline just described.

Much of the southern shore of the Long Beach peninsula has been developed as a Town of Smithtown recreation center. In the western corner, is a Town owned mooring basin with a launching ramp and space for about 130 boats. To the east, is a marina shared by the private Smithtown Bay Yacht Club (with space for 105 boats) and the Town of Smithtown "Little Africa" marina (with 110 berths). At the marina there is also a Town launching ramp (Figure 9). Directly north of the marina is the Town owned Little Africa Park, which extends the width of Long Beach, to Smithtown Bay. A 0.1 km2 (20 acre) tract on the eastern tip of Long Beach, owned by the Village of Nissequogue, is the site of the Nissequogue Wildlife Preserve.

Access to the preserve is limited because it is a fragile environment and the site of an important heron rookery and piping plover nesting sites.

Along the northern shore of Long Beach, fronting on Smithtown Bay, are two Town of Smithtown beaches: at Long Beach Town Park (697 m or 2284 ft long) and at Little Africa Town Park (185 m or 605 ft long). There are about 26 private houses on Long Beach between Little Africa Town Park and the Nissequogue Wildlife Preserve. Only a few of the houses are on the harbor or bay shoreline. There are three stone groins along the Smithtown Bay shoreline. One groin (50 m or 163 ft long) is in Long Beach Town Park, one (23 m or 75 ft long) at the eastern end of Little Africa Town Park and the third (28 m or 90 ft long) a few hundred meters further east in a Town right-of-way.