Microscopic X-ray florescence spectrometry (μXRF) can be used to obtain the information on distribution and correlation of the chemical elements in the biogeochemical samples. The information is useful in revealing conditions of material formation, dynamic processes of elemental distribution and correlation among them, as well as biological metabolism. A laboratory μXRF spectrometer was developed with combining a polycapillary microfocus X-ray beam excitation with a rhodium anode (50 kV, 1 mA), a silicon drift detector (SDD) and three-dimensional scanning capability. The angle between the sample stage and the SDD detector was designed to be adjustable so that an in situ determination of a heterotypic sample, such as geological samples, can be made with the μXRF set. A rock-biofilm sample was taken from a field investigation, where there is a small mine and the rock in a shallow pool was covered by a green biofilm. The rock-biofilm sample was stored in a refrigerator for further μXRF measurement. Maize seeds were from markets. Dry maize seeds and ones with Pb-soaked were sliced before the μXRF measurements. Then, the developed laboratory μXRF spectrometer was applied to study the mobilization of lead in the rock-biofilms, and location of K, Ca, Mn, Fe, Cu, Zn and Pb in germination of the maize seeds. We found that (1) Pb accumulated in biofilms with a bioaccumulation factor of 1.7. (2) Pb increased gradually from rock to biofilm, and then decreased from biofilm to air. A peak occurred in the biofilm. (3) In maize seeds without Pb-soaked, K, Ca, Mn, Fe, Cu, Zn and Pb were detectable. Zn was mainly found in endosperm, a small amount of Zn in embryo; trace Fe was detected in endosperm and embryo; Trace Pb was detectable in endosperm, not in embryo. (4) In germination of maize seeds soaked with dilute Pb solution, K was detected in both endosperm and embryo; Fe was distributed in seed coat and endosperm; Cu and Zn were in endosperm; most of Pb occurred in embryo and especially accumulated in fresh roots, which implies that the accumulation of Pb in roots functions as tolerance of detoxification of toxic elements in seed germination.