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The canal connects the South Shore and North Shore waters and has a lock to deal with tidal differences. When the locks are open the water is quite rapid and you need to run well above the 5 MPH speed posted when approaching the tide gates/locks. When run south you need to watch out for a rapid right near the rail road bridge.
I post this after seeing a number of unknowing boater run into trouble.
i run it all the time and thats good advice and will add when they are open and the water is running leave plenty of room between you and the boat in front of you to allow for the screw ups. i have seen people change their mind at the very last second and try to turn around right before entering and have seen boats that lose control and play ping pong off the sides as they go through. i personally would rather run them while they are open no matter how fast the water is running than lock through 3 wide with people who have no idea what they are doing. i keep the locks phone # with me and will call from ocean if i know they are closed to check on the traffic and will wait if its crazy.
Been through it plenty. Gets pretty sporty when the locks are open. (esp with big tide phases) You will get 6 knots of current, 3 foot standing waves and traffic in both directions.
Boaters get in trouble when they get scared and slow down. People gowing down current back off the throttle and cant steer. People going up current need to power through.
Mayhem has the best advice. Give yourself plent of room before you enter and power through. Hesitation gets you in trouble here.
I run through those locks at least a dozen times a season and I'm amazed at how dangerous the conditions can sometimes be. That's a hugely important point about having good separation going north when the locks are open, wake that bounces off the walls from a semi-planing boat in front of you can make for standing, breaking, 2-3 foot waves in addition to an incredibly fast current.
I've never understood why they let the current rip through there so often, especially on busy weekends. It can't just be about waiting times as I've encountered the situation equally when its busy or not busy. Originally I know the locks were kept open to increase salinity in Shinnecock bay but that was before the SH inlet broke through. Doesn't it seem that when the current is fastest is when the tidal difference is greatest and thus, when the locks should be closed the most? It seems random, I've even been in the locks for literally less than 1 minute sometimes when the water levels were basically equal.
Sometimes I (jokingly) think the lock operators are just bored and want to see some action but there must be some reason to let those hazardous conditions exist? I know the marina owners and Tiderunners would be happier with calmer conditions. I used to be intimidated by the conditions, now I only get worried when its busy, there are a lot of inexperienced captains going through their with no idea what to expect.
is there plenty of water up inside after you pass thru locks,also whats bridge height ? probably going to run a 35 duffy with a tower thru locks if i have clearance havent looked at chart yet an never been thru locks any info would be great. looking for a good weather window around first week of march
v70cat, we fish but also enjoy all the spots to anchor off and relax for the day.spend time in greenport,orient near bug light and everything in between. last year when out with my 11 year old i put 98 miles on the boat looking for fluke when it was too rough outside. wound up east of the ruins out in gardiners. Seawags-not sure if you are talking about a tower on top of a flybridge if thats the case you might not have the clearance as most of the larger boats have to lower the outriggers when going through.
According to this railroad bridge limits clearance to 22+/- feet.
The Shinnecok Bay has some high spots with 4+/- feet depth. Many 40 foot plus sport fishermen boat run the bay without trouble, just don't go into the inter coastal waterway west of the bridge by the Cost Guard Station.
Shinnecock Canal, NY 
