Terrestrial diatoms are an integral component of the soil microbial community. However, their productivity and how it compares to other algal groups remains poorly known. This lack of knowledge hampers their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal and spatial patterns of diatom assemblages and the role of environmental factors on the soil diatom productivity. We collected soil algal samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 12 months. The algal abundances were then derived from pigment analysis using High-Performance Liquid Chromatography. Our results indicate that diatom productivity is mainly controlled by factors related to soil moisture availability leading to seasonal patterns, whereas the concentration of green algae remained stable over the course of the study period. Generally, anthropic disturbed habitats contained less living diatom cells than undisturbed habitats. Also, we learned that diatoms can be the dominant algal group at periods of the year with high soil moisture.