Here is a (partial) list of common underwater acoustics reference books.
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Ainslie, M.A., Principles of Sonar Performance Modeling, Springer (2010).
A modern treatment of both man-made and bio-sonar. Includes derivations of the active and passive sonar equations from physical principles.
Au, W.W.L., The Sonar of Dolphins, Springer (1993).
The first ever book describing the hearing and echo location of dolphins.
Au, W.W.L. and M.C. Hastings, Principles of Marine Bioacoustics, Springer (2008).
Thorough treatment of hearing and echo location in marine mammals.
Bjørnø, L., Applied Underwater Acoustics, Elsevier. (2017)
Advanced topics in underwater acoustics.
Blondel, P., The Handbook of Sidescan Sonar, Springer (2009).
Theory and practice of sidescan sonar.
Boyles, C.A., Acoustic Waveguides: Applications to Oceanic Science, Wiley (1984).
A thorough treatment of normal modes in ocean acoustics.
Brekhovskikh, L.M. and Y.P. Lysanov, Fundamentals of Ocean Acoustics, Springer-Verlag (2003).
Excellent, readable book on both the math and the physics.
Brekhovskikh , L.M. and O.A. Godin, Acoustics of Layered Media (I & II), Springer-Verlag (1990).
Very mathematical presentation; probably difficult reading for many but contains a wealth of useful results.
Burdic, W.S., Underwater Acoustic System Analysis, Prentice-Hall (1991).
A nice balance between signal processing and acoustics; as the title says, basically what you need to know to understand and design acoustic systems.
Carey, W.M. and R.B. Evans, Ocean Ambient Noise: Measurement and Theory, Springer (2011).
Theory and practice of ocean noise.
Cole, R.H., Underwater Explosions, Dover (1965).
A thorough treatment of underwater explosions.
DeSanto, J., Scalar Wave Theory: Green's Functions and Applications, Springer-Verlag (1992).
A nice, mathematical presentation of graduate level material on waves.
DiFranco, J.V. and W.L. Rubin, Radar Detection, Prentice-Hall (1968).
Everything you ever needed to know about statistical detection theory applied to radar but the mathematical theory for individual applies unchanged to sonar.
Etter, P.C., Underwater Acoustic Modeling and Simulation: Principles, Techniques and Applications, E&FN Spon (Chapman & Hall), (2003).
Probably the best book for an overview of specific noise, propagation, and reverb models, but pricey. Less theory and implementation information than JKPS.
Frisk, G.V., Ocean and Seabed Acoustics: A Theory of Wave Propagation , Prentice-Hall (1994).
A mathematical treatment, emphasizing stratified problems.
Godin, O.A. and D.R. Palmer, History of Russian Underwater Acoustics, World Scientific (2008).
Historical summary of theoretical and practical developments in underwater sound in Russia.
Hunt, F.V., Electroacoustics : The Analysis of Transduction, and its Historical Background, AIP (1954).
Theory and historical account of electro-acoustic transducers.
Horton, J.W., Fundamentals of SONAR, 2nd edition, United States Naval Institute (1959).
A fine predecessor to Urick's classic.
Jackson, D.R. and M.R. Richardson, High-Frequency Seafloor Acoustics (2006).
Everything you ever needed to know about the interaction of high frequency sound with the seabed.
Jensen, F., W. Kuperman, M. Porter, and H. Schmidt, Computational Ocean Acoustics, Springer-Verlag (2000)
Details about the numerical implementation and use of ocean acoustic models. (Errata for this book is also available)
Katsnelson, B.G., V.G. Petnikov and J.F. Lynch, Fundamentals of Shallow Water Acoustics, Springer (2012).
The study of how low and medium frequency sound propagates and scatters on the continental shelves of the worlds oceans, with practical applications
Katsnelson , B.G. and V.G. Petnikov, Shallow Water Acoustics, Springer (2002).
A readable overview of all aspects of shallow water acoustics.
Lee, D. and M.H. Schultz, Numerical Ocean Acoustic Propagation in Three Dimensions, World Scientific (1995).
Emphasizes the math/numerical issues more than the physics.
Leighton, T.G., The Acoustic Bubble , Academic (1994).
Everything you ever needed to know about the acoustical properties of gas bubbles.
Lurton, X., Introduction to Underwater Acoustics: Principles and Applications , Springer (2010).
Covers similar ground to Urick's classic, from a more modern perspective.
Medwin, H. and C.S. Clay, Fundamentals of Acoustical Oceanography, Academic Press (1998).
Covers ocean acoustics quite broadly but is particularly useful for material on scattering by objects, bubbles, and boundaries.
Munk, W., P. Worcester, and C. Wunsch, Ocean Acoustic Tomography , Cambridge (1995).
Great book on the subject by the pioneers of the field.
Richardson, W.J., C.R. Greene, C.I. Malme and D.H. Thompson, Marine Mammals and Noise , Academic (1995).
Pioneering text documenting all aspects of the influence of underwater sound on marine mammals.
Ross, D., Mechanics of Underwater Noise (1990).
A classic text on radiated noise from ships.
Sherman, C. and J.L. Butler, Transducers and Arrays for Underwater Sound,Springer (2007).
Electro-acoustic transducers and arrays.
Simmonds, J., and D.N. MacLennan, Fisheries Acoustics: Theory and Practice (2005).
Theory and practice of fisheries sonar.
Tolstoy, I. and C.S. Clay, Ocean Acoustics: Theory and Experiment in Underwater Sound, AIP (1987).
Theory and practice of underwater sound.
Tolstoy, A., Matched-Field Processing, World-Scientific (1993).
The only overview book available on MFP. A nice, readable introduction to the basics.
Urick, R.J., Principles of Underwater Sound, 3rd Edition, Peninsula (1983).
A classic book on the subject. Despite being one of the first books, it's still a key reference with large parts of the material unavailable elsewhere. Behind the engineering treatment is clearly a solid understanding of the science behind things.
Physics of Sound in the Sea, Peninsula Publishing (originally published in 1945).
Emphasizes the physics. They knew an awful lot already by 1945.
Zimmer, W.M.X., Passive Acoustic Monitoring of Cetaceans, CUP (2011)
How to count whales by listening to the sounds they make.
ACTA ACUSTICA united with ACUSTICA (Publication of the European Acoustics Association).