A hydrodynamic model of Upper Klamath and Agency Lakes, Oregon, was used to explore the effects of the operation of proposed offstream storage at Long Lake Valley on transport of larval suckers through the Upper Klamath and Agency Lakes system during May and June, when larval fish leave spawning sites in the Williamson River and springs along the eastern shoreline and become entrained in lake currents. A range in hydrologic conditions was considered, including historically high and low outflows and inflows, lake elevations, and the operation of pumps between Upper Klamath Lake and storage in Long Lake Valley. Two wind-forcing scenarios were considered: one dominated by moderate prevailing winds and another dominated by a strong reversal of winds from the prevailing direction. On the basis of 24 model simulations that used all combinations of hydrology and wind forcing, as well as With Project and No Action scenarios, it was determined that the biggest effect of project operations on larval transport was the result of alterations in project management of the elevation in Upper Klamath Lake and the outflow at the Link River and A Canal, rather than the result of pumping operations. This was because, during the spring time period of interest, the amount of water pumped between Upper Klamath Lake and Long Lake Valley was generally small. The dominant effect was that an increase in lake elevation would result in more larvae in the Williamson River delta and in Agency Lake, an effect that was enhanced under conditions of wind reversal. A decrease in lake elevation accompanied by an increase in the outflow at the Link River had the opposite effect on larval concentration and residence time.