To test the hypothesis that internal ion imbalances at high pH are caused by altered branchial ion transporting capacity and permeability, radiotracers (24Na+ and 36Cl-) were used to measure ion movements across the gills of intact rainbow trout (Oncorhynchus mykiss) during 3 d exposure to pH 9.5. At control pH (pH 8.0), the trout were in net ion balance, but by 8 h at high pH, 60%-70% reductions in Cl- influx (JClin) and Na+ influx (JNain) led to net Cl- and Na+ losses of -200 micromol kg-1 h-1. Outflux (diffusive efflux plus renal ion losses) was not initially altered. By 72 h, net Cl- balance was reestablished because of a restoration of JClin. Although JNain remained 50% lower at this time, counterbalancing reductions in Na+ outflux restored net Na+ balance. One-substrate ion-uptake kinetics analyses indicated that reduced ion influx after 8 h at pH 9.5 was caused by 50% decreases in Cl- and Na+ maximal transport rates (JClmax, JNamax), likely reflecting decreased numbers of functional transport sites. Two-substrate kinetic analyses indicated that reduced internal HCO-3 and H+ supply for respective branchial Cl-/base and Na+/acid transport systems also contributed to lower JClin and, to a lesser extent, lower JNain at pH 9.5. Recovery of JClmax after 3 d accounted for restoration of Cl- balance and likely reflected increased numbers of transport sites. In contrast, JNamax remained 33% lower after 3 d, but a lower affinity of the gills for Na+ (fourfold greater KNam) accounted for the chronic reduction in Na+ influx at pH 9.5. Thus, reestablishment of Cl- uptake capacity and counterbalancing reductions in Na+ outflux allows rainbow trout to reestablish net ion balance in alkaline waters.