Persistent pools in intermittent streams of the semi-arid Pilbara region of northwest Australia are important biogeochemical hotspots and refugia for aquatic biota during dry periods. Allochthonous nutrient inputs are significant in short periods of connected flow, although processes of nutrient recycling, hyporheic interactions and evapoconcentration within disconnected pools are of increasing importance in maintaining primary production during no-flow periods. While it has been widely assumed that productivity of Pilbara streams is strongly phosphorus (P) limited, low amounts of dissolved inorganic nitrogen (DIN) in streams across the region suggest that nitrogen (N) is also potentially limiting. Here, we investigated the importance of N and P limitations on pools with and without alluvial groundwater connectivity in a Pilbara stream. We used in-situ bottle incubations and a 13C-enriched NaHCO3 isotopic tracer to measure production changes in response to nutrient amendments. Charophyte production was 2 mg C g-1 DW h-1 while water column production was orders of magnitude less (~0.01 mg C g-1 DW h-1). Although charophytes showed no clear respiration response to short-term nutrient addition, productivity was positively correlated to both charophyte N and P content (R2 = 0.65, p < 0.001 and R2 = 0.41, p < 0.001 respectively). This relationship was stronger in pools which were disconnected from alluvial groundwater (N: R2 = 0.92, p < 0.001 and P: R2 = 0.77, p < 0.001). Short-term water column production was N limited in some pools (F > 7.6, p < 0.009) but this was not linked to alluvial inputs. Clearly both N and P, along with alluvial groundwater connectivity, have significant and complex roles in regulating production in these pools and build on our understanding of semi-arid intermittent streams.