Clinal variation occurs at three polymorphic enzyme loci in a population of the threespine stickleback, Gasterosteus aculeatus, from the Brush Creek drainage, a small coastal system in northern California, U.S.A. The drainage consists of two tributary streams, representing two broad ecological units based on stream gradient, which meet at a coastal lagoon. Seven localities were sampled once each year for three years, and the allele frequencies for alcohol dehydrogenase (Adh), glucophosphate isomerase (Gpi-2), and phosphoglucomutase (Pgm) were estimated for each sample by gel electrophoresis. At each locus, all samples were in Hardy-Weinberg equilibrium, and there was no evidence for temporal heterogeneity. There was significant spatial heterogeneity detected for all three loci, which was particularly strong for Pgm. Although the degree of differentiation in allozyme frequencies differed among the three loci, the overall patterns of differentiation were very similar for all three. The similarity of spatial patterns of differentiation is explained by population processes, such as natural selection and gene flow; linkage disequilibrium among the loci was not detected. The allelic diversity within the drainage was very high, and the distribution of alleles among localities suggested that the rate of gene flow within the drainage was relatively high. These data suggest that the allozyme dines, as well as a parallel dine for the ratio of lateral plate morphs, are maintained in their current ecotonal position by gene flow across the ecotone with differential selection on either side. However, the history of the drainage suggests that the dines originated when isolated stickleback populations inhabiting ecologically distinct habitats within the drainage came into secondary contact.