In many estuarine sites, morphological and genetic differences between anadromous and freshwater threespine sticklebacks are maintained despite breeding in sympatry. Here, we investigate the maintenance of this morphological divergence in a natural hybrid zone in the River Tyne, Scotland. We provide a morphological description of the hybrid zone, and using a Bayesian MCMC approach, identified distinct anadromous and freshwater genetic clusters. Anadromous and freshwater sticklebacks breed in spatial and temporal sympatry in the lower reaches of the River Tyne. The frequency of hybrids within these sites (33%) indicates prezygotic isolation is not complete, and suggests that assortative mating is not strong. However, significant heterozygote deficit and cytonuclear disequilibrium in juveniles collected from sympatric sites confirms that barriers to gene flow exist between the morphs in the wild. In addition, we found no evidence of a directional bias in hybridisation, although hybrids with anadromous mothers were more common because anadromous females outnumbered freshwater females within the hybrid zone. We discuss the potential contribution of temporal, spatial, and sexual prezygotic barriers to the observed reproductive isolation as well as postzygotic selection against hybrid zygotes or fry.