In Sealion discussions it is always said that German submarines would be useless in the Channel, and certainly the planned German deployment reflected this. The Germans had a submarine designed for coastal waters, the Type II, which made up about half of their submarine force. It was a small submarine with a displacement of 250 tons. These were the only ones they planned to put in the Channel.
So what did the British have?
The British had three types of submarines operational in September 1940 – the Grampus, Parthian, and U Class. A fourth class of submarine, the V class, wasn’t ordered until 1941.
The Grampus Class (5 subs) was a minelayer that carried a total of 12 torpedoes in six torpedo tubes at the bow. It was used extensively to supply Malta. All were sunk in the Mediterranean. It was too large for coastal operations, at 1,760 tons.
The Parthian Class (6 subs) was meant to be a long range patrol submarine for Far Eastern Waters, but most of them were sunk in the Mediterranean. At 1,760 tons, it was too big for the Channel.
The U Class was originally meant to be a training and target submarine but found to be useful for operations in the North Sea. It was much smaller, at 630 tons. 15 might have been available in September 1940. 34 more were ordered, starting in March 1940, but the first of these wasn’t delivered until November 1940.
So, for British submarines, we have a total of 15 just about suitable for work in the Channel, however, checking each on Uboat.net we find:
HMS Undine – lost 7 Jan 1940
HMS Unity – Lost 29 Apr 1940
HMS Ursula – Patrolling Channel on anti-invasion duties 20 September 1940
HMS Umpire – Launched 30 Dec 1940, not available
HMS Una – Launched 1941, not available
HMS Unbeaten - Commissioned 10 November 1940, not available
HMS Undaunted – Commissioned 30 Dec 1940, not available
HMS Union – launched 1941, not available
HMS Unique – Commissioned 27 September 1940, partly available, though training and trials not completed until 24 October, when she moved to Portsmouth.
HMS Upholder – the most famous sub in the RN, not commissioned until 31 October 1940, not available.
HMS Upright – not Commissioned until 3 Sept 1940, finished training 26 September and moved to Portsmouth, arriving 30 September – available(just), patrolled English Channel.
HMS Urchin – not launched until 30 Sept 1940, not available
HMS Urge – Commissioned 12 Dec 1940, not available
HMS Usk – Commissioned 11 October 1940, not available
HMS Utmost – patrolling English Channel 25 September 1940, available
HMS P32 – Commissioned 3 May 1941, not available
HMS P33 – Commissioned 30 May 1941, not available
HMS P 36 – Commissioned 24 Sept 1941, not available
All the others were commissioned in 1941 or 1942 even if they were ordered in 1940.
So, only three (really two) British submarines were available for use against the invasion forces in the Channel. If they were firing torpedos at barges, it is likely the torpedos would go under the barges because of their shallow draft, but they could do some damage to the other ships in the invasion force.