We demonstrate the fabrication of three-dimensional (3-D) hollow microstructures embedded in photostructurable glass by a nonlinear multiphoton absorption process using a femtosecond (fs) laser. Fs laser direct writing followed by annealing and successive wet etching in dilute hydrofluoric (HF) acid solution resulted in the rapid manufacturing of microchips with 3-D hollow microstructures for the dynamic observation of living microorganisms and cells in fresh water. The embedded microchannel structure enables us to analyze the continuous motion of Euglena gracilis. A microchamber with a movable microneedle demonstrates its ability for the elucidation of the information transmission process in Pleurosira laevis. Such microchips, referred to as nano-aquariums realize the efficient and highly functional observation of microorganisms and cells.