There's no answer for MJ's new found water powers, until Spidey follows Hydro-Man to his underwater lab.... only it turns out she's really a clone, and so's Hydro-Man. It seems that Allistair Smythe hired Miles Warren to use his cloning technology, except it wasn't perfected. Basically as a test, Warren went to the place where Hydro-Man "died" and took a cell from the water type substance. So, a Hydro-Man clone is born. When Bench read a paper involving Mary Jane's disappearance, he told Warren to make an MJ clone. Warren went to her apartment and got a hairstrand from her comb, before the accident. The MJ clone is made, but she flees Warren's lab (the same one used by Norman Osborn, the Green Goblin) and finds Peter. The rest is history. Anyway, a big battle occurs, in which Hydro-Man and MJ degenerate, and Warren flees, with a part of Spidey's costume with blood on it. Spidey's alone again. While on the GWB, Madame Web plucks Spidey away. She tells him that the time has arrived, and that he must do her bidding since she knows where Mary Jane is.
Recap from DRG4's Spider-Man the Animated Series Page