Jessica is one of Bryce's many victims, and therefore has motive. As a reminder, back in season one Bryce rapes a mostly unconscious Jessica at a party, and later she tries to bring him to justice at the trial that unfolds in season two. Her efforts, though brave, don't pan out the way she'd hoped (aka with Bryce in jail for the foreseeable future).
In season three she takes this frustration out by running for student body president and starting the Hands Off Our Bodies club at school with female classmates, who incite a riot during the school's Homecoming game. Was Jessica pushed to the edge again that night at the docks, ultimately murdering Bryce? Yes and no.
Not long after Zach leaves Bryce broken and bloody by the pier, Jessica arrives not with her on-again boyfriend Justin, but with her ex, Alex, in order to pick up whatever Bryce had wanted to give her (the blood-splattered confession and apology cassette tape, that he asks Jessica to play for Mrs. Baker). In full-on "pity me" mode as usual, Bryce groans that although he's trying to be better, "this f*cking world won't let me . . . nobody believes I can change." (Sure, Jan.) Given how badly beaten Bryce is, Alex makes a move to help him up and save him from either bleeding out or dying of exposure in the Winter air even though Jessica wants to leave him. That's when things start to go down hill for the villain.
"F*cking Zach! I'm gonna f*ck up his other knee and wreck his life," he yells in "a fury of pain," as Ani tells it, before accusing Jessica of setting him up to get attacked by Zach. That's when something becomes clear to Alex — if Bryce survives this ordeal, Zach isn't the only one whose life he's going to try to destroy. Bryce is going to go after Jessica, and even Alex, too. That's what inspires Alex to make a final, murderous decision.
"You've hurt everyone I ever loved," Alex tells Bryce, before shoving him into the ice-cold water below. There Bryce, given his extensive injuries, struggles to stay afloat as Alex and Jessica watch from the safety of the pier, ignoring his pleas for help. Finally, Bryce sinks down for good, leaving the pair to reckon with their choice.