In remote, tropical areas human influences increase, potentially threatening pristine seagrass systems. We aim (i) to provide a bench-mark for a near-pristine seagrass system in an archipelago in East Kalimantan, by quantifying a large spectrum of abiotic and biotic properties in seagrass meadows and (ii) to identify early warning indicators for river sediment and nutrient loading, by comparing the seagrass meadow properties over a gradient with varying river influence. Abiotic properties of water column, pore water and sediment were less suitable indicators for increased sediment and nutrient loading than seagrass properties. Seagrass meadows strongly responded to higher sediment and nutrient loads and proximity to the coast by decreasing seagrass cover, standing stock, number of seagrass species, changing species composition and shifts in tissue contents. Our study confirms that nutrient loads are more important than water nutrient concentrations. We identify seagrass system variables that are suitable indicators for sediment and nutrient loading, also in rapid survey scenarios with once-only measurements.