You activate a portal by beating the shadow creatures that came out of it. You can't warp to any portals after you jump into Lake Hylia before you activate the portal in Zora's Domain. You probably can't warp after the Bridge of Eldin gets sucked up before you activate another portal either. You can't warp before you're asked to warp the bridge to Kakariko Gorge either. There are 4 things you can warp with to the portal where it's supposed to go, the wooden bridge, the stone bridge, the meteorite, and the cannon. You can't warp to the Bridge of Eldin without the stone bridge when the stone bridge is not there or to Kakariko gorge without the wooden bridge when the wooden bride is not there. In all other cases, you can warp to any portal you already activated when you're in wolf form. In general, any time you go under a portal you haven't already activated, shadow creatures will come out of it. There are some exceptions. They will not come out in Ordon Spring until you beat the Faron twilight. The ones at the bridge of Eldin will not come out until you blow up the boulders just north of it. They will not come out in Lake Hylia until after you get the lanayru vessel of light. They will not come out in Upper Zora River until you talk to the woman just outside the door in human form. They will not come out in the Sacred Grove until you go through the Lost Woods the second time.