Barriers to prevent spawning migrations of sea lampreys Petromyzon marinus remain an important component of an integrated sea lamprey management program in the Laurentian Great Lakes. Concerns about effects on nontarget fishes have led to the construction of specially designed vertical-slot trap-and-sort fishways to mitigate potential barrier effects. To improve passage at these fishways, we used passive integrated transponder technology to assess the performance of two fishways located on low-head sea lamprey barriers. Fishways on the Big Carp River (which flows into Lake Superior) and Cobourg Brook (which flows into Lake Ontario) were assessed for attraction efficiency, trap attraction and retention, and passage efficiency. Based on the results of these assessments, fishways were modified by increasing the trap volume and altering the funnel characteristics to reduce escapement from the trap and then reassessed. Attraction efficiency for all tagged fish was high (≥80%) at both sites in all years. Fishway modifications improved passage from 35% in 2003 to 88% and 64% in 2004 and 2005, respectively, at the Big Carp River. As expected, white suckers Catostomus commersonii, an obligate migrant, had higher attraction and passage efficiency, fewer passage attempts, and shorter migration delay than did rock bass Ambloplites rupestris, a facultative migrant. No improvements were seen at Cobourg Brook, where passage efficiency remained low (7% in 2003, 10% in 2005), probably because of the loss of attraction flow. At both fishways, individual fish averaged 3-10 attempts to pass through the fishways and had their migrations delayed 1-2 weeks. The observed improvements to the Big Carp River fishway, which resulted in high fishway attraction and passage rates for white suckers, suggest that vertical-slot fishways can help mitigate the effects of low-head barriers for some species. Our study provides a rigorous quantifiable approach to assessing fishway performance that can be employed widely and successfully to assess initial fishway design and subsequent modifications.