Previous research identified distinct genetic, life-history and reproductive differences between populations of common bully (Gobiomorphus cotidianus) upstream and downstream of a pulp and paper mill outfall on the Tarawera River in the Bay of Plenty, New Zealand. This thesis sought to investigate the distribution of amphidromous and non-amphidromous common bully in the Tarawera River by examining fish collected from upstream (37 km inland) and downstream (20 km inland) locations and comparing them to fish from similar inland locations (40 km and 17 km inland, respectively) in the nearby Rangitaiki River. Otolith microchemistry revealed life-history differences between upstream and downstream populations and stable isotope analysis ensured long-term site residency. Amphidromy dominated in the downstream river populations, while the disappearance of diadromous fish generally occurred with inland distance. A mixture of diadromous and non-diadromous fish were found in the upstream Rangitaiki, while a complete absence of diadromous recruits was found in the upstream Tarawera River. A reduction in oculoscapular canal structures also coincided with loss of diadromy in fish from both rivers. Temporal reproductive divergence was investigated through track annual trends in gonadosomatic index. The Tarawera River receives significant inputs from numerous industrial, municipal and natural sources, most notably from two pulp and paper mills. In the absence physical barriers in the Tarawera, it has been hypothesised that the lack of diadromous recruits in the upstream Tarawera River may be related to aquatic discharges in the downstream river. A behavioural study was performed to examine the hypothesis that pulp and paper mill effluent may be acting as a chemical barrier to fish migration within the river. A dual-choice chamber was employed to examine the responses of common bully exposed to a range of effluent concentrations (100, 50, 25, 12.5, 0% v/v). Fish exhibited significant avoidance responses when exposed to 100 and 50% effluent concentration, while no avoidance was observed at effluent concentrations below 50% This study demonstrated that common bully show a strong preference for river water when simultaneously exposed to effluent, albeit at environmentally unrealistic concentrations (i.e. greater than 15%), implicating potential for this effluent to act as a chemical barrier in the Tarawera River. Following the establishment of reproductive timing of common bully in the Tarawera River, a wild fish health assessment was undertaken to investigate the effects of long-term effluent exposure in situ. Adult common bully were sampled downstream of the mill influence and compared to an appropriate reference population from the downstream Rangitaiki River. Male and female fish from the Tarawera River demonstrated 6- to 9-fold greater ethoxyresorufin-O¬-deethylase (EROD) activity compared to reference fish, indicating exposure to organic contaminants in this river. Tarawera females showed some minor variation in hematological variables including decreased mean cell volume (MCV), mean cell haemoglobin (MCH) and increased total white blood cell count (WBCC) suggestive of an immune response. Slightly greater ovarian follicular steroid production in Tarawera fish potentially indicates some form of endocrine alteration. However, this response may also be related to differences in reproductive synchrony and gonadal development between the two fish populations.