Estimating the absolute entropy of water at room temperature
To evaluate $S=Nk\ln(\Omega)$ it is necessary to use statistical mechanics to calculate $\Omega$. 

In quantum mechanics, for any independent system in a potential there is generally a set of permissible energy levels $\epsilon_1,\,\epsilon_2,\cdots$. The energy of the whole assembly of $N$ similar systems is $E$ and the volume $V$. The number of microstates or configurations (complexions) is $\Omega$ and this depends on $E,\,V,\, N$. It is assumed that all of the different microstates with the same values of $E,\,V,\,N$ are equally probable.

There are $n_1$ systems with energy $\epsilon_1$, $n_2$ systems with energy $\epsilon_2$ and so on. The total number of different states of the assembly is the number of ways of dividing $N$ things into groups with $n_1, n_2\cdots$ in each which is $N!/(n_1!n_2!\cdots)$. The total number of different states is then the  total of all of these and is

$$\sum_{\text{all possible sets }n_i} \frac{N!}{\prod_i n_i}$$

As the total energy $E$ is fixed as is $N$, then 

$$\Omega = \sum \frac{N!}{\prod_i n_i}  \quad \text{with constraints} \quad \sum_i n_i =N, \sum_i \epsilon_i n_i=E$$

This is a difficult expression to evaluate but it happens that the largest term makes such an overwhelming contribution that only this term need be considered. The mathematical method to find the maximum is an interesting use of Lagrange's method of undetermined multipliers and is given in texts on stat mech but covers several pages so is too long to include here. 

The result is that 

$$S=k\left(N\ln\left(\sum_i e^{-\epsilon_i /(kT)}  \right) +\frac{E}{kT}\right) $$

where $\displaystyle Z=\sum_i e^{-\epsilon_i /(kT)}$ is the partition function. The entropy thus comes down to calculating the partition function. In fact all other thermodynamic properties can be found once $Z$ is known.

In a molecular system the $\epsilon_i$ are the energies of translation, vibration and rotation and electronic excited states (if any). Knowing the energy levels, say from spectroscopy, then allows each of these terms to be calculated. The translational partition function is calculated using the Sakur-Tetrode equation and a value $\ln(Z)\approx 70 $ is typical. For rotational motion $\ln(Z)\approx 10$ and for vibrations $\ln(Z)\approx 1.5$ for each vibrational mode. The vibrational contribution is small because at room temperature $kT\approx 210$ wavenumbers and vibrations are typically several hundred to a few thousand wavenumbers.  In the case of liquid water you have a particular problem which may be mitigated somewhat by adding H bonds to a molecule as an extra vibration.