This study was conducted in Gibson Jack Creek (42.7843°, -112.448°) a headwater stream located in the Caribou-Targhee National Forest, Pocatello, Idaho. Gibson Jack Creek is a tributary of the Portneuf River, that flows into the Snake River, which ultimately flows into the Columbia River. It drains a large area within the Bannock Range (~ 16.1 km2 from Portneuf confluence) with elevations ranging from ~1500 to 2200 m. The climate is semi-arid steppe, with annual mean temperature ranging from below 0 to 35 °C and precipitation from 38 to 76 cm, 65 % of which is snowfall. The vegetation on the south-facing slope is mostly sagebrush, grass, and juniper, with mostly coniferous trees on the north-facing slop. The bedrock consists of quartzite and shale in the northern portion and limestone in the south and the soil is composed primarily of silt loam, fine sandy clay loam and gravel. This synoptic survey was designed in support of the sampling goals of the Aquatic Intermittency effects on Microbiomes in Streams (AIMS) Project. During June 2023, a field team co-collected datasets characterizing the hydrology, biogeochemistry, and ecology across 50 locations within a sub-drainage of Gibson Jack Creek. The sites were selected to balance multiple competing priorities: (i) strategically targeting existing monitoring infrastructure with long-term data; (ii) including sites near several known springs and tributary junctions; and (iii) including a range of drainage area and topographic wetness index (TWI) values, both of which have been correlated with flow permanence. Briefly, the sites selected based on drainage area and TWI were chosen by binning drainage area into 10 bins and then binning TWI into quintiles within each drainage area bin. We then randomly selected a point in each bin after accounting for points selected based on existing infrastructure, springs, and tributaries; and enforcing a minimum spacing of 100 m between locations. We then made minor adjustments to points to account for field conditions, for instance adjusting locations with respect to a road crossing. Water (if present), biofilm, leaf litter and sediment samples were collected at each location. This data comprises the ash free dry mass (AFDM) of two sample type namely leaf litter and sediment. Wet mass of leaf litter or sediment were recorded, and the subsamples dried at 70 °C for 48 h and re-weighed. Dry subsamples were combusted at 500 °C for 2 h and re-weighed. AFDM was calculated as the ratio of the organic matter combusted to the dry mass of each sample.