Filamentous algae nutrient scrubbers (FANS) have potential as a novel on-farm treatment system to remove and recover diffuse nutrients from agricultural drainage water. FANS use attached filamentous algae that grow and assimilate nutrients from the water which are removed when algal biomass is harvested for beneficial use (e.g. biofertilizer, animal feed supplement). This thesis investigated the attachment abilities, growth rates, biomass productivity and nutrient removal rates of four locally isolated filamentous algae species with the potential for use on FANS to bioremediate nutrients in agricultural drainage water. To date, a standardised method to assess the productivity and nutrient removal of attached filamentous algae and identify target species for FANS cultivation has not been developed. Therefore, a reproducible bioassay was developed to rapidly assess the ability of four filamentous algae species to attach and grow, remove nutrients, and produce harvestable algal biomass using microscale FANS (μFANS) under controlled indoor conditions. This bioassay included the development of a method for rapid seeding by ‘hooking” algal filaments onto the FANS liner to provide initial physical attachment. Within 14 days, a “lawn” of the seeded algae had established and the “hooked” biomass had attached biologically onto the FANS liner. Oedogonium sp. Was identified as the best performing species overall, with the strongest holdfast attachment, high biomass productivity and high nutrient removal rates. As the growth and bioremediation performance of filamentous algae can vary with seasonal changes in environmental conditions, the performance of four filamentous algae species was assessed under summer and winter ambient outdoor conditions on mesocosm-scale FANS. Oedogonium sp. Had the highest biomass productivity and nitrate removal rates under both seasons, confirming it as the best performing species. In addition, Oedogonium sp. FANS had the lowest contamination in percentage cover of non-target species compared to the other three species under both summer and winter conditions. These results demonstrate that Oedogonium sp. Has a higher tolerance than the other three species to summer and winter ambient temperature and light variation, enabling Oedogonium sp. To maintain dominance on the floway for a longer period. For these reasons, Oedogonium sp. Was identified as a promising target for year-round cultivation on FANS. FANS operating parameters can strongly influence algal biomass productivity and nutrient removal. Therefore, the effects of the influent flow rate, harvesting frequency and initial standing crop on unialgal Oedogonium sp. FANS biomass productivity and nutrient removal performance were assessed under controlled environmental conditions to remove any variability in performance due to variations in ambient conditions. Results suggested that an initial standing crop of 70-80 g DW m-2, harvesting frequency of four days and influent flow rate of 1 L min-1 (16.7 L min-1 .m width) were optimal for Oedogonium sp. Cultivated on FANS to maximize biomass productivity and nutrient removal under controlled laboratory conditions. These results contribute to understanding the impacts of operating parameters on optimizing unialgal Oedogonium sp. FANS biomass production and nutrient removal performance. Despite their potential influence on performance, the effects of FANS seeding methods and species composition have received little attention. Therefore, the effects of seeding method (controlled seeding vs. natural establishment) and seeded species composition (single species vs. mixed species algal assemblages) were investigated in FANS treating agricultural drainage on a dairy farm over seven months. FANS seeded using controlled seeding established biomass five times faster (10 days) than FANS left to establish naturally (7 weeks). Overall, the seeding method and species composition of algae seeded on FANS did not significantly affect biomass productivity and nutrient removal performance. However, FANS seeded with a single species (Oedogonium sp.) had a lower contamination rate in terms of percentage coverage of non-target species than FANS seeded with a mixed species assemblage. These results demonstrate that controlled seeding and cultivation of a single target filamentous algae species can help to maintain a higher abundance of a target species on FANS over a longer period of time, enabling the recovery of high-quality biomass with low variation in algae species composition. This thesis has demonstrated that FANS can be successfully used to treat nutrients in agricultural drainage water, and therefore could be implemented as a novel tool to assist in mitigating diffuse pollution in New Zealand. The findings can be used to provide farmers and land managers with a clearer understanding of how FANS can be used to remove nutrients from agricultural drainage water to meet water quality objectives while minimizing the impacts on farming activities.