Sediments, microbial mats, biofilms and other microbial communities are characterized by steep gradients of physical and chemical parameters. Fibre optical microsensors, microoptodes, that we developed over the last three years have become powerful tools to investigate and measure these parameters with a sufficient spatial resolution and with a minor disturbance of the micro-environment in natural systems. Together with microoptodes for oxygen, pH, temperature we developed a sensitive measuring system that enables the measurement of luminescence intensities and lifetimes of indicators that are immobilized at the tip of tapered fibers. As light sources, we used light emitting diodes, that nowadays are available with a high optical power output even in the blue part of the spectrum, where many indicators can be excited. Furthermore, LEDs are easy to modulate and thus enable both, the measurement of luminescence intensities independent of ambient light and the measurement of luminescence lifetimes based on a phase modulation technique. The weak amount of light emitted at the tip of a dip-coated silica-silica fibre required, however, a photomultiplier tube (PMT) as detector. Although the PMTs are very sensitive light detectors, the application in natural systems for measurement of concentration profiles with and without strong ambient light causes additional noise problems with the PMT. Therefore, we improved the composition of the sensing layer that covers the tapered fibre tip and the taper geometry, because both have a large impact on the signal (see abstract of Kohls et al.). Furthermore, we improved the optical setup to reduce inherent coupling losses and inherent noise signals like unwanted additional luminescence caused by epoxy, solvents etc.