This document is prepared for fisheries biologists, managers and administrators concerned with lagoon fisheries and aquaculture. Our main objective is to draw attention to the need for greater understanding of relationships between the hydraulics and productivity of lagoon fish and shellfish. The fishery yields from lagoons vary widely, and, probably, predictably, once such relationships are understood. Furthermore, the productivities of many lagoons could probably be enhanced by hydraulic manipulations, but the hydraulic manipulation is presently risky, except in dystrophic lagoons. The document includes a description of lagoon physics, how hydraulics are likely linked to lagoon productivity, how lagoons might be expected to respond to hydraulic alterations, and a protocol for physical investigations. This latter is a necessary step to protect as well as enhance fisheries and aquaculture resources in lagoons, which are especially vulnerable to degradation and overexploitation.