Nanoscale surface films are known to develop on surfaces exposed to natural waters and have potential impacts on many environmental processes. A new method using atomic force microscopy is presented which physically removes the developed film in a defined area and then quantifies the difference in height between the film and the area where the film has been removed. The difference gives the absolute thickness of the surface film, which has not previously been measured. Suwannee River humic acid was exposed to substrates, and the surface film thickness as a function of pH and exposure time was measured. Discrete and very small colloids in the range 1-5 nm were observed as expected, and these sat on a coherent surface film, not the original mica substrate. Low pH values of 2 gave rise to relatively thick surface films of about 3 nm, although these films were not continuous at higher pH values. At pH 4.8, the film thickness increased with exposure time up to about 5 h and did not subsequently increase. The maximum film thickness measured was about 1 nm at that pH. The method is applicable to the measurement of many environmental surfaces, although resolution will depend on the substrate and film roughness.