We're not sure what is inside Pluto and Charon — this is one of the reasons to send New Horizons to find out! But scientists can make an educated guess about the bodies' interiors by answering a few questions:
We know some pieces of the puzzle but other pieces are still missing or poorly described. Uncertainties in the basic statistics of radius and density frustrate scientists' attempts to build models of the interiors of Pluto (especially) as well as Charon. This figure shows some ideas of their interiors.
Given the large amount of rock and the planet's size, scientists expect that the process of the planet forming and the natural radioactivity of the rock inside will have heated the interior sufficiently to melt the ice and allow it to separate from the rock. The rock inside Pluto has likely settled into a core surrounded by a thick shell or mantle of ice, as illustrated in the figure. Pluto and Charon together are estimated to be about 65% to 70% rock (including metal) and about 30% to 35% ice or material close to ice in density, which could mean liquid water or organic matter. (The word "organic" here simply means carbon-bearing and does not imply "living.") Very volatile ices (nitrogen, methane and carbon monoxide) are concentrated at Pluto's surface, but whether they form a distinct crust is unknown.
An intriguing possibility is that an ocean of liquid water underlies Pluto's icy shell. The ocean may be mixed with or overlie an organic-rich layer (not shown in the diagram). Could building blocks for life exist at this very edge of the solar system? There is evidence that icy moons of Jupiter and Saturn have hidden oceans, and our improved understanding of heat generation and transport in icy worlds makes this a real possibility for Pluto.
Life as we know it requires three things:
Pluto's surface is far too cold for liquid water, but its interior is probably warm and maintained that way by the slow decay of naturally occurring elements such as uranium, potassium-40 and thorium.
Enough heat is released that a water ocean may exist between the rocky core of Pluto and its thick outer layer of ice. Planetary scientists have long thought that icy satellites might possess oceanic layers underneath their surface ice layers. The discovery by the Galileo orbiter that Europa, Callisto and possibly Ganymede possess interior oceans, along with similar inferences from the Cassini mission for Titan and Enceladus, greatly increases our expectation that Pluto also possesses an ocean. Pluto's ocean is also likely to contain biogenic elements in a solution, especially if it is in contact with an organic-rich layer.
Where Pluto may not pass astrobiological muster is in the matter of sufficient energy to power life. Pluto's ocean would be dark and cold - near-freezing. Even if in contact with a rock core, it is likely that this modest core is today insufficiently hot to be volcanically active or even to drive hydrothermal circulations. So it is difficult to argue for a deep biosphere on Pluto today. On the other hand, it is also true that Pluto's rock core was much hotter and probably active in the geological past, so it is not unreasonable to speculate that some form of primitive, microbial life may have evolved long ago and just might have once plied the "Styxian seas" of Pluto.
Since Charon is smaller and less dense than Pluto, its internal structure is simpler to model. But its smaller size, paradoxically, makes its internal structure more uncertain. The figure above illustrates a Charon that is differentiated in a similar fashion to Pluto - separated into a mantle of ice and core of rock. But we also cannot rule out the possibility that Charon has a roughly uniform mixture of rock and ice all the way through - that is, undifferentiated - as in the lower figure, or something in between.
New Horizons will help find out which (if any) of these ideas are correct by measuring the masses, densities and shapes of Pluto and Charon as well as searching for clues in the surface geology of "what lies beneath."