Beam-based elemental assays target a particular age or date range in the sectioned otolith, and thus take advantage of the chronological growth sequence recorded in the otolith. These types of targeted assays have proven to be popular among those reconstructing migration histories and identifying nursery areas, as well as those using Sr:Ca ratios to infer temperature history. The advantages of an age-structured approach are obvious, particularly since the beam sizes of the current generation of instruments approach the width of a typical daily increment. As a result, the assay can be limited to the time scale of interest, whether it is weekly, annual or at an intermediate scale. Disadvantages of the approach include the requirement for sectioning to expose the growth sequence, the potential for contamination from the sectioning and polishing procedure, and some degree of beam penetration into underlying growth layers. However, the most significant disadvantage is the reduced sensitivity and precision of beam-based assays compared to their solution-based counterparts.

There are a wide variety of sophisticated instruments available for probed assays of the otolith, but the most frequently used include the energy-dispersive (ED-EM) and wavelength-dispersive (WD-EM) electron microprobes, proton-induced X-ray emission (PIXE), and laser ablation ICPMS (LA-ICPMS). No one instrument type is sensitive to each element, nor is any one instrument preferred for use in all assays. In general however, the minor elements such as Na and K can only be measured accurately with an electron microprobe, while the trace elements require PIXE or LA-ICPMS.

Reconstruction of migration histories using the elemental composition along an otolith growth sequence is similar in many respects to stock discrimination based on analysis of the otolith core, and shares many of the same assumptions. However, migration analysis expands the scope of the interpretation, by linking a series of elemental assays along an otolith transect to the growth chronology recorded in the otolith, thus allowing the reconstruction of migration pathways structured by age or date. In principle, migration analysis is one of the most powerful applications of otolith microchemistry, although its successes to date have been largely limited to the detection of anadromy. Subtler migration patterns are now being detected with LA-ICPMS, which is more sensitive to non-physiologically regulated trace elements. Previously reported difficulties in interpreting migration histories may have been due to the use of the electron microprobe, which is more suited to assays of physiologically-regulated elements.

Several forms of migration analysis have been reported. One of the most successful has been the comparison of elemental trajectories among fish in search of a common history, or alternatively, the determination of the age or date at divergence. This is a particularly robust application, since it requires no knowledge of the fish's past environment, and is relatively insensitive to any ontogenetic shifts in otolith elemental composition which may have occurred. In many respects, this comparative approach is analogous to the use of elemental fingerprints as biological tracers, as described earlier. A potentially more powerful approach is one in which the otolith elemental trajectory is linked to shifts in temperature and water chemistry along possible migratory routes. Such an approach is the basis for the detection of anadromy using Sr:Ca ratios, in which the shift between freshwater and saltwater environments is so marked in the otolith as to be virtually unambiguous. Similar interpretations in more homogeneous environments appear possible, but are complicated by the assumption that a given elemental concentration at any point along an otolith transect reflects the environment in the same way. In other words, ontogenetic changes in otolith elemental composition are assumed not to exist. Yet such changes have been clearly documented, even in fish held under constant environmental conditions. As a result, observed trends in concentration across an otolith could reflect either a shift in the fish's environment, an age-related change in incorporation rate independent of the environment, or both. With further experimentation, it should be possible to factor out ontogenetic shifts in elemental composition, thus simplifying the interpretation of possible migration pathways. To date however, it is not always clear from published reports whether reconstructed distributions have been adjusted for ontogenetic effects.