First, let us consider flux.

Flux is the amount of something passing through a surface multiplied by the area of that surface. It can be a fluid, gas, electric field, or anything that can be described by a vector field. In the picture below, there are F liters/minute of water flowing in the circular pipe.

If we were to consider an imaginary surface slicing perpendicularly through the pipe (surface A), the flux through that circular surface would be F liters/minute multiplied by the area of the circle. It is important to note that that if we were to consider a surface slicing through at a bias (like surface B), the flux would be the same. Even though the elliptical area is larger than the circular one the amount of flux per unit area is less because the flux is no longer perpendicular to the surface. Flux through an area is then defined as $$ \Psi = \vec{F}\cdot\vec{A} = \|\vec{F}\|\|\vec{A}\|\cos\theta $$ where the vector area \( \vec{A} \) is defined to be normal to the surface. For a surface that is open, the choice of which of the two normal vectors we mean is arbitrary (we just have to be consistent). For a closed surface, the normal is defined to point to the outside of the surface. The angle \(\theta\) is the angle between the area-normal and the vector \(\vec{F}\). You can see as the angle between the flow and the surface gets closer to \(\frac{\pi}{2}\) that the flux gets smaller and smaller until it vanishes completely when the two are perpendicular.
Now, consider the volume defined by surfaces A, B and the walls of the pipe in the figure
above. We can define the total flux through the volume as
$$ \Psi_{total} = \Psi_{pipe} + \Psi_A + \Psi_{B} $$
Unless we have a leaky pipe, \(\Psi_{pipe} = 0\). Because we define the surface normal
of a closed surface to point **outward**, the flux through surface A is negative
(the flow and the normal are in opposite directions, so the dot-product is negative).
The flow through B is equal in magnitude to that passing through surface B but positive.
Hence, \(\Psi_{total} = 0 \). This makes intuitive sense when dealing with conservation of
mass as otherwise there would be an accumulation of mass inside the pipe
(\(\Psi_{total} < 0\)) or loss of mass (\(\Psi_{total} > 0\)).

Divergence is the amount of flux leaving a closed surface as the volume of the closed surface approaces zero. So, we now look at the general sitution of the pipe above in cylindrical coordinates. We consider a small enough closed volume that we can consider it a cube. In order to compute the total flux, we have to do 6 integrations as there are 6 sides to a cube. But we will group them in pairs, one pair for each direction \(\rho, \phi, z\).

The vector field in cylindrical coordinates is given by $$ \vec{F} = F_{\rho} \unitv{\rho} + F_{\phi} \unitv{\phi} + F_{z} \unitv{z} $$ We place our tiny cube-like volume in the field \(\vec{F}\) at some point \(\vec{P}=(\rho,\phi,z)\).

First we consider the flux passing through the surfaces normal to the \(z\) direction (the
top and bottom faces of the cube). Since the distances involved are small, we can approximate
the field passing through these as
$$ F_{top} = F_z(\rho,\phi,z + \Delta z) \approx F_z(\rho,\phi,z) + \pard{F_z}{z}(\rho,\phi,z)\frac{\Delta z}{2} $$
It should be noted that the other components of the field don't play a part here because they
are parallel to these surfaces so nothing going in the, say, \(\rho\) direction leaves
via the \(z\) direction. Similarly for the bottom surface,
$$ F_{bottom} = F_z(\rho,\phi,z - \Delta z) \approx F_z(\rho,\phi,z) - \pard{F_z}{z}(\rho,\phi,z)\frac{\Delta z}{2} $$
The areas of these surfaces are equal and independent of \(z\).
$$ A_z = \rho\Delta\phi\Delta\rho $$
Therefore, the flux through these z-surfaces is (remembering that the flux through the bottom
surface is into the volume and so is negative)
$$ \Psi_z = F_{top}A_z - F_{bottom}A_z = (F_{top} - F_{bottom})A_z $$
$$ \Psi_z = (F_z + \pard{z}{F_z}\frac{\Delta z}{2} - (F_z - \pard{F_z}{z}\frac{\Delta z}{2}))\rho\Delta\phi\Delta\rho $$
$$ \Psi_z = \pard{F_z}{z}\rho\Delta \phi \Delta\rho \Delta z $$
Recognize that the term \( \rho\Delta \phi \Delta\rho \Delta z \) is the differential volume in cylindrical
coordinates, so we can write the previous equation as
$$
\begin{equation}
\label{eq:fluxz}
\Psi_z = \pard{F_z}{z}\Delta V
\end{equation}
$$
Where \(\Delta V\) is the differential volume element.
I should note that if you were to do this derivation in Cartesian coordinates, the x and y component derivations would
be identical (except for the subscripts). But in cylindrical coordinates, things get a little more interesting from
here on out.
Looking now at the \(\phi\) direction we consider the front and back faces of the volume. (I will omit the function
arguments to the partial derivatives in the service of brevity with the understanding that we are talking about
the point \(P=(\rho,\phi,z)\)).
$$ F_{back} = F_\phi(\phi + \Delta \phi) \approx F_\phi + \pard{F_\phi}{\phi}\frac{\Delta \phi}{2} $$
$$ F_{front} = F_\phi(\phi - \Delta \phi) \approx F_\phi - \pard{F_\phi}{\phi}\frac{\Delta \phi}{2} $$
$$ A_\phi = \Delta\rho\Delta z $$
Because the positive \(\phi\) direction is toward the back of the volume,
$$ \Psi_{\phi} = (F_{back} - F_{front})A_{\phi} $$
$$ \Psi_{\phi} = (F_\phi + \pard{F_\phi}{\phi}\frac{\Delta \phi}{2} - (F_\phi - \pard{F_\phi}{\phi}\frac{\Delta \phi}{2}))\Delta\rho\Delta z $$
$$ \Psi_{\phi} = \pard{F_\phi}{\phi}\Delta\phi\Delta\rho\Delta z $$
The term \(\Delta\phi\Delta\rho\Delta z\) is *almost* the differential volume. And maybe because we know where
we are headed, we bend the equation to our will
$$ \Psi_{\phi} = \pard{F_\phi}{\phi}\Delta\phi\Delta\rho\Delta z = \pard{F_\phi}{\phi}\frac{\rho}{\rho}\Delta\phi\Delta\rho\Delta z $$
$$
\begin{equation}
\label{eq:fluxphi}
\Psi_\phi = \frac{1}{\rho}\pard{F_\phi}{\phi}\Delta V
\end{equation}
$$
Now we try to handle the \(\rho\) component. We need to be careful here. But first things first. The vector
field is defined similarly to previous components.
$$ F_{right} = F_\rho(\rho + \Delta \rho) \approx F_\rho + \pard{F_\rho}{\rho}\frac{\Delta \rho}{2} $$
$$ F_{left} = F_\phi(\rho - \Delta \rho) \approx F_\rho - \pard{F_\rho}{\rho}\frac{\Delta \rho}{2} $$
Here is where it gets tricky. The area definitions are different because *the two surfaces are not equal in size* and so must
be treated differently.
$$ A_{right} = (\rho+\frac{\Delta\rho}{2})\Delta\phi\Delta z $$
$$ A_{left} = (\rho-\frac{\Delta\rho}{2})\Delta\phi\Delta z $$
First computing the flux on the right side.
$$ \Psi_{right} = F_{right}A_{right}=(F_\rho + \pard{F_\rho}{\rho}\frac{\Delta \rho}{2})((\rho+\frac{\Delta\rho}{2})\Delta\phi\Delta z) $$
$$ \Psi_{right} = (F_\rho + \pard{F_\rho}{\rho}\frac{\Delta \rho}{2})(\rho\Delta\phi\Delta z + \frac{1}{2}\Delta\rho\Delta\phi\Delta z) $$
$$ \Psi_{right} = F_\rho\rho\Delta\phi\Delta z+\frac{1}{2}F_\rho\Delta\rho\Delta\phi\Delta z + \frac{1}{2}\pard{F_\rho}{\rho}\rho\Delta\rho\Delta\phi\Delta z + \frac{1}{4}\pard{F_\rho}{\rho}\Delta\rho^2\Delta\phi\Delta z $$
Similarly on the left hand side
$$ \Psi_{left} = F_{left}A_{left}=(F_\rho - \pard{F_\rho}{\rho}\frac{\Delta \rho}{2})((\rho-\frac{\Delta\rho}{2})\Delta\phi\Delta z) $$
$$ \Psi_{left} = (F_\rho - \pard{F_\rho}{\rho}\frac{\Delta \rho}{2})(\rho\Delta\phi\Delta z - \frac{1}{2}\Delta\rho\Delta\phi\Delta z) $$
$$ \Psi_{left} = F_\rho\rho\Delta\phi\Delta z-\frac{1}{2}F_\rho\Delta\rho\Delta\phi\Delta z - \frac{1}{2}\pard{F_\rho}{\rho}\rho\Delta\rho\Delta\phi\Delta z + \frac{1}{4}\pard{F_\rho}{\rho}\Delta\rho^2\Delta\phi\Delta z $$
Computing \(\Psi_\rho\) (finally, after all that algebra) by subtracting and cancelling terms
$$ \Psi_\rho = \Psi_{right} - \Psi_{left} $$
$$ \Psi_\rho = F_\rho\Delta\rho\Delta\phi\Delta z + \pard{F_\rho}{\rho}\rho\Delta\rho\Delta\phi\Delta z $$
We make the same modification to the first term that we did with \(\Psi_\phi\) and substituting \(\Delta V\)
$$
\begin{equation}
\label{eq:fluxrho}
\Psi_\rho = \frac{1}{\rho}F_\rho\Delta V + \pard{F_\rho}{\rho}\Delta V
\end{equation}
$$
This last equation is correct but we normally don't see it written this way, so we factor out a \(\frac{1}{\rho}\) and invoke
the reverse chain rule.
$$ \Psi_\rho = \frac{1}{\rho}(F_\rho + \rho\pard{F_\rho}{\rho})\Delta V = \frac{1}{\rho}\pard{}{\rho}(\rho F_\rho)\Delta V $$
And so the total flux through our tiny volume is
$$ \Psi_{total} = \Psi_\rho + \Psi_\phi + \Psi_z = \left(\frac{1}{\rho}\pard{}{\rho}(\rho F_\rho) + \frac{1}{\rho}\pard{F_\phi}{\phi} + \pard{F_z}{z}\right)\Delta V $$
The divergence is the ratio of the flux through a closed surface as the volume of that closed surface approaces 0.
$$ \nabla\cdot\vec{F} = \lim\limits_{\Delta V \to 0} \frac{\Psi_{total}}{\Delta V} = \frac{1}{\rho}\pard{}{\rho}(\rho F_\rho) + \frac{1}{\rho}\pard{F_\phi}{\phi} + \pard{F_z}{z} $$