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Bouguer anomaly - This anomaly corrects for the gravitational attraction of the rock above sea level.

This correction is done after Free Air correction which accounts to the height of the measurements above sea level.

The simple Bouguer correction is calculated assuming that the rock above sea level is a slab of uniform thickness and density (generally 2.67g/cc for land data, 2.0 or 2.2 for marine data).

This density is called reduction density, and can be calculated with the Nettleton method which states that the optimum density is the one with the least correlation with topography.

In case of rough terrains a Complete Bouguer Correction is needed which accounts for topographic lows and highs (Terrain Correction).

The Bouguer anomaly is best for looking at local and regional gravity anomalies.

Isostatic anomaly - The isostatic anomaly accounts for low density roots needed to balance the topography and can be derived using either Pratt's or Airy's hypothesis and corresponds to the deviation of the crustal structure from floating statically in the upper mantle.

The isostatic anomaly improves on the other 2 anomaly models by taking into consideration the root structure under the crustal structure (mountain range) but that is also a problem as we often don't know what the root looks like.

This type of anomaly is best for the study of the sedimentary sequence, while it is not appropriate for deep crustal studies.

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Q: What is the difference between isostatic anomaly and Bouguer anomaly?
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