Marginal coastal soils are dependent on appropriate land management to prevent soil erosion, as a result of low soil stability combined with exposure to strong winds. An example of such an area is the machair, a fixed dune system utilized for agriculture in the northwest of Scotland, UK. The separate and combined effects of synthetic NPK fertilizer and a traditional soil conditioner (kelp, a seaweed) on soil structure formation, stabilization and biological parameters were studied on a cropped field on the machair. Soil physical properties examined included water retention at 10 kPa matric suction, water stable aggregates (WSA) > 1 mm, aggregate stability, and biological properties including ester-linked fatty acid (ELFA) analysis and beta-glucosidase activity for microbial biomass and activity, respectively. Significant treatment effects were few and inconsistent between sampling times, but included kelp and/or NPK fertilizer reducing aggregation, water retention, microbial biomass and activity relative to the unamended control treatment. Furthermore, seasonal variation, which could be attributed to changes in soil water content, was stronger than variation in response to fertilizer treatments. Principal components analysis of the ELFA data showed that ploughing promoted fungal biomass relative to bacteria, and confirmed both the absence of consistent synthetic and organic fertilizer effects and the sensitivity of microbial biomass to season. Overall, the study demonstrated the resilience of a calcareous sandy soil to amendment with fertilizer.