Ok, got home to my books, so here is some more information about the Soviet u-boat efforts in the Baltic during WW2. This is all taken from "Sjöfront" by Per-Olof Ekman (in swedish, ISBN 951-50-0244-3).
During the Winter war, the Soviet u-boat fleet got its first chance to show what it could. They had around 30 u-boats active in the Baltic, but due to the short season, harsh weather, and most important of all, minimal experience, results were poor. Only a dozen actually participated in the action, and they managed to sink 5 steamers. Of these, 2 were neutrals (one swedish, one estonian) and 2 were German (with which Soviet at this time had the non-aggression Molotov-Ribbentrop pact). One ship was Finnish. All but one of the ships were sunk from the surface with the deck gun.
By the start of WW2, the Soviet u-boat arm was the biggest in the world, but many of the u-boats were obsolete. When Germany attacked Soviet, they had 68 u-boats in the Baltic, but after the initial retreat, only around 40 were left. Most were lost to mines, but German submarines took a few, and many were scuttled in harbor. The Russians managed to sink one German u-boat (U-144) Aug 10 1941. Mines laid by Soviet submarines sunk a few steamers, and October 30 SC323 managed to get a torpedo in the German s/s Baltenland, which started burning and ran ashore.
During the winter 41-42 the u-boats lay hidden in Leningrad, and the crew either maintained the boats or fought the Germans on the frontlines of beseiged Leningrad. During 1942 around 30 u-boats were ready for service, 10 at any one time.
The Finns and Germans of course prepared for the Soviet u-boats, and minefield had been laid. The Germans, however, did not anticipate much from the Soviet side, and did not complete the defence with u-boat nets, schnellboot patrolling etc, even though Finnish requests. Germany was tasked with securing the strategically important islands Lavansaar, Penisaari and Seiskari (for monitoring ship activity in the Gulf of Finland), but the troops planned for this operation were sent to the Leningrad front instead. The islands stayed in Soviet hands for the whole war. The island of Hogland, near the middle of the Gulf, was secured by Finland after an attack over the ice. The Germans laid around 1,800 mines in the "Nashorn" barrage, and around 2,000 in the "Seeigel" barrage. New mines were later that summer added. The Finnish "Rukajärvi" barrage consisted of 619 mines at different depths in 4 lines. Later some 700 mines were added. "Paljärvi" had around 100 mines. Several hundred mines were also put more offensively near Kronstadt either by speedboats or by bombers. The road through the Gulf of Finland to the hunting grounds of the Baltic Sea was a dangerous 427 km for the Soviet u-boats.
Three Soviet u-boats were lost (2 due to mines, 1 to enemy action) on the first 10-boat campaign; the campaign claimed 8 freight ships (15 745 brt): 3 German, 2 Finnish and 3 Swedish. The second 10-boat group managed to sink 7 merchant ships (14 078 brt, one was Swedish); 1 soviet u-boat was destroyed. The third, and last, group before the winter, consisted of 16 u-boats. They onlt managed 4 ships (again, one of the neutral Sweden), and 8 u-boats were lost (the 3 Finnish submarines each managed to destroy one Soviet u-boat). After this setback the russians didn't anymore try to interdict traffic in the Ahvenanmeri area. The soviets managed to sink 18 ships (37 789 brt) during the 1942 campaign. Total losses for Axis ships (i.e. also including mines and other disasters) was 0,3%. Five ships were under Sweidsh flag, even though Soviet sub commanders had orders to not attack Swedish ships. Identification was of course very hard during the dark and stormy nights most succesful attacks took place. The swedish iron ore transports was a prime Soviet target.
1943 started with 20 soviet u-boats ready. The Germans this time put much more effort into protecting the Baltic against the Soviet u-boat threat. Even though the losses had been small, the psychological effect was large. The Germans did not want to use ships for escort duty, and they wanted use a safe Baltic as training grounds for their warships. In late March a 30 nautical miles long, 60-90 meters deep, double submarine net was laid straight over the Gulf of Finland. Gaps between islands close to the coast were filled with smaller nets. The "Nashorn" mine barrage now had around 8,500 mines."Seeigel" had 1,300 mines, and "Rukajärvi" 800. It turned out that the u-boat net was much more effective than the huge mine barrages. A large number of surface boats and coastal artillery watched over the Gulf. 3 soviet u-boats tried to force though the net, but failed; 2 were sunk by depth charges. After this, no new attempt were made before August, when the nights became dark, but again both of the 2 subs sent out were destroyed. The Russians then changed tactic, and thanks to heavy air support managed to sweep a way through "Seeigel", but the net was still there. No Soviet u-boats managed to enter the Baltic during 1943.
1944 began with the Germans sending a large number of surface ships to the Gulf of Finland to protect the minefields and the submarine net. Due to no air cover, losses were high to Soviet aircraft and speedboats, but the Germans held the line until the general retreat during the autumn of '44. One lost soviet submarine and another damaged kept the Soviet subs in harbour until October.
Finland signed peace with Soviet 19.9.1944. This prompted the Germans to try to take over the Finnish-occupied Hogland in the middle of the Gulf, in operation "Tanne Ost". Hogland was defended by 1,712 Finnish soldiers, but most of the artillery and heavy equipment had been withdrawn in anticipation of a Soviet occupation of the island. The Germans attacked with 2,300 men. It was a disaster. 37 Finns were killed, and the Germans lost 153 men on the island and an unknown number lost on the 7 destroyed landing craft and gunboats. The Finns took 1,231 prisoners.
Now, with the Finnish out of the war, the Russians finally had a safe way into the Baltic, and 10 u-boats steamed out in early October. The results did not match those of 1942.
In the last stages of the war, over 2 million Germans were transported with ships from pockets along the coast. Losses were proportionally small, but Soviet subs sunk three big passenger ships, which still are the largest maritime catastrophes of the world. Wilhelm Gustloff (25 484 brt) had over 8,000 passengers (of which the majority were civilians) when it was sunk 30.1 by S13. Only 964 survived. The same sub sunk s/s Steuben ten days later, with 2,000 wounded and 1,000 refugees onboard. 300 survived. And finally April 17 the sub L3 sunk s/s Goya with 7,000 on board, of which 183 survived. The sub commander was awarded the Golden Star. All in all 17,000 persons were killed in these 3 sinkings. The "tonnage king" Konovalov, however, got nothing. He had come out of favour with the political leadership after some scandals (one episode in Turku during the new year of 1945 was the beginning of his end). He was later degraded, sacked, and sent into the gulags for 3 years. He was pardoned after Stalin's death.
When the war was over in 1945, 29 Soviet u-boats were left.