The excretion of nitrogenous waste products in the form of ammonia (NH3) and ammonium (NH4 +) is a fundamental process in aquatic organisms. For mytilid bivalves, little is known about the mechanisms and sites of excretion. This study investigated the localization and the mechanisms of ammonia excretion in mytilid mussels. An Rh protein was found to be abundantly expressed in the apical cell membrane of the plicate organ, which was previously described as a solely respiratory organ. The Rh protein was also expressed in the gill, although at significantly lower concentrations, but was not detectable in mussel kidney. Furthermore, NH3/NH4 + was not enriched in the urine, suggesting that kidneys are not involved in active NH3/NH4 + excretion. Exposure to elevated seawater pH of 8.5 transiently reduced NH3/NH4 + excretion rates, but they returned to control values following 24 h acclimation. These mussels had increased abundance of V-type H+-ATPase in the apical membranes of plicate organ cells; however, NH3/NH4 + excretion rates were not affected by the V-type H+-ATPase specific inhibitor concanamycin A (100 nmol l−1). In contrast, inhibition of ciliary beating with dopamine and increased seawater viscosity significantly reduced NH3 excretion rates under control pH (8.0). These results suggest that NH3/NH4+ excretion in mytilid mussels takes place by passive NH3 diffusion across respiratory epithelia via the Rh protein, facilitated by the water current produced for filter feeding, which prevents accumulation of NH3 in the boundary layer. This mechanism would be energy efficient for sessile organisms, as they already generate water currents for filter feeding.