To reduce the water footprint of microalgae biomass production, it is essential to recycle the culture medium. The influence of medium recycling on the performance of the cyanobacterium Arthrospira platensis, the most widely cultivated microalgae, was investigated. Arthrospira was harvested with a 20 μm mesh size microstrainer, which is the benchmark harvesting technology for Arthrospira production. Repeated recycling of the culture medium resulted in a decline in growth rate and the maximum quantum yield of photosynthesis (Fv/Fm) when compared to a control culture in fresh medium. This decline was accompanied by accumulation of organic matter in the culture medium (up to 104 mg C L− 1). This organic matter consists of 70% of sugars, mostly rhamnose-rich polysaccharides with uronic acids. Accumulation of polysaccharides resulted in a decrease in the filtration rate through the microstrainer used for harvesting. Part of the biomass escaped harvesting and was returned to the culture with the recycled medium. This resulted in a change in the Arthrospira population and reduction in the harvesting efficiency, but this change in population had no effect on the growth rate. The growth rate of Arthrospira in the recycled culture medium was primarily influenced by organic matter that accumulated in the medium.