Complete macrophyte removal to maintain drainage performance in lowland streams can have a negative effect on resident fish communities, but few studies have quantified this impact. Moreover, limited research has been carried out exploring alternative approaches for macrophyte removal that minimise the impact on the resident fish community. The aims of this study were (i) to determine how the current practice of removing almost 100% of available macrophyte cover affects native fish populations in lowland New Zealand streams and (ii) to see whether this impact can be reduced by limiting macrophyte removal to alternating 50-m sections of the waterway. Native fish populations were surveyed before and after experimental macrophyte removal for the following three treatments: (i) complete macrophyte removal, (ii) macrophyte removal from alternating 50-m reaches and (iii) control with no macrophyte removal. Radiotelemetry was used to monitor the behavioural response of individual giant kokopu (Galaxias argenteus) to the different treatments. The results of this study suggest that current drain management practices reduce CPUE of fish by 60%. Although limiting macrophyte removal to alternating 50-m sections did not minimise the community impacts of drain clearing, large giant kokopu did benefit from this strategy. All tagged giant kokopu remained in stream reaches partially cleared of macrophytes, while in completely cleared reaches all individuals were displaced. These results demonstrate the threat current drain management practices pose to New Zealand native fish and highlight the value of trialling alternative methods of macrophyte removal.

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